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root/OpenMD/trunk/src/applications/dynamicProps/DynamicProps.cpp

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 917 by tim, Fri Mar 24 17:29:07 2006 UTC vs.
Revision 1604 by jmichalk, Mon Aug 8 18:53:40 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include <iostream>
#	Line 46 | Line 46
46		#include "brains/Register.hpp"
47		#include "brains/SimCreator.hpp"
48		#include "brains/SimInfo.hpp"
49	+	#include "utils/StringUtils.hpp"
50		#include "utils/simError.h"
51
52		#include "applications/dynamicProps/DynamicPropsCmd.h"
#	Line 53 | Line 54
54		#include "applications/dynamicProps/RCorrFunc.hpp"
55		#include "applications/dynamicProps/VCorrFunc.hpp"
56		#include "applications/dynamicProps/LegendreCorrFunc.hpp"
57	+	#include "applications/dynamicProps/RadialRCorrFunc.hpp"
58	+	#include "applications/dynamicProps/ThetaCorrFunc.hpp"
59	+	#include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
60	+	#include "applications/dynamicProps/EnergyCorrFunc.hpp"
61	+	#include "applications/dynamicProps/StressCorrFunc.hpp"
62	+	#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
63
64
65	<	using namespace oopse;
65	>	using namespace OpenMD;
66
67		int main(int argc, char* argv[]){
68
#	Line 72 | Line 79 | int main(int argc, char* argv[]){
79
80		//get the dumpfile name and meta-data file name
81		std::string dumpFileName = args_info.input_arg;
75	–
76	–	std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
77	–
82
83		std::string sele1;
84		std::string sele2;
#	Line 82 | Line 86 | int main(int argc, char* argv[]){
86		if (args_info.sele1_given) {
87		sele1 = args_info.sele1_arg;
88		}else {
89	<	char*  sele1Env= getenv("OOPSE_SELE1");
89	>	char*  sele1Env= getenv("SELECTION1");
90		if (sele1Env) {
91		sele1 = sele1Env;
92		}else {
93		sprintf( painCave.errMsg,
94	<	"neither --sele1 option nor $OOPSE_SELE1 is set");
95	<	painCave.severity = OOPSE_ERROR;
94	>	"neither --sele1 option nor $SELECTION1 is set");
95	>	painCave.severity = OPENMD_ERROR;
96		painCave.isFatal = 1;
97		simError();
98		}
#	Line 97 | Line 101 | int main(int argc, char* argv[]){
101		if (args_info.sele2_given) {
102		sele2 = args_info.sele2_arg;
103		}else {
104	<	char* sele2Env = getenv("OOPSE_SELE2");
104	>	char* sele2Env = getenv("SELECTION2");
105		if (sele2Env) {
106		sele2 = sele2Env;
107		} else {
#	Line 105 | Line 109 | int main(int argc, char* argv[]){
109		}
110		}
111
112	+	// use the memory string to figure out how much memory we can use:
113	+	char *end;
114	+	long long int memSize = memparse(args_info.memory_arg, &end);
115	+	sprintf( painCave.errMsg,
116	+	"Amount of memory being used: %llu bytes\n", memSize);
117	+	painCave.severity = OPENMD_INFO;
118	+	painCave.isFatal = 0;
119	+	simError();
120	+
121		//parse md file and set up the system
122		SimCreator creator;
123	<	SimInfo* info = creator.createSim(mdFileName, false);
123	>	SimInfo* info = creator.createSim(dumpFileName, false);
124
125
126		TimeCorrFunc* corrFunc;
127	<	if (args_info.dcorr_given){
128	<	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
127	>	if(args_info.sdcorr_given){
128	>	corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
129	>	} else if (args_info.dcorr_given){
130	>	corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
131		} else if (args_info.rcorr_given) {
132	<	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
133	<	}
134	<	else if (args_info.vcorr_given) {
135	<	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
132	>	corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
133	>	} else if (args_info.r_rcorr_given) {
134	>	corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
135	>	} else if (args_info.thetacorr_given) {
136	>	corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
137	>	} else if (args_info.drcorr_given) {
138	>	corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
139	>	} else if (args_info.vcorr_given) {
140	>	corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
141	>	} else if (args_info.helfandEcorr_given){
142	>	corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
143	>	} else if (args_info.stresscorr_given){
144	>	corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
145		} else if (args_info.lcorr_given) {
146		int order;
147		if (args_info.order_given)
#	Line 125 | Line 149 | int main(int argc, char* argv[]){
149		else {
150		sprintf( painCave.errMsg,
151		"--order must be set if --lcoor is set\n");
152	<	painCave.severity = OOPSE_ERROR;
152	>	painCave.severity = OPENMD_ERROR;
153		painCave.isFatal = 1;
154		simError();
155		}
156
157	<	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
157	>	corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
158		}
159
160		if (args_info.output_given) {

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords):
Revision 917 by tim, Fri Mar 24 17:29:07 2006 UTC vs.
Revision 1604 by jmichalk, Mon Aug 8 18:53:40 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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